Error analysis of the poisson P3M force field scheme for particle-based simulations of biological systems

David Marreiro; Shela Aboud; Marco Saraniti; Robert Eisenberg

doi:10.1007/s10825-005-7134-5

Error analysis of the poisson P³M force field scheme for particle-based simulations of biological systems

David Marreiro, Shela Aboud, Marco Saraniti, Robert Eisenberg

Research output: Contribution to journal › Article › peer-review

3 Scopus citations

Abstract

The ability to accurately simulate electrolyte solutions is a strong requirement for the modeling of charge transport in ion channels. In this work, a Particle-Particle-Particle-Mesh (P³M) algorithm is used to model the electrostatic interactions governing the physics of electrolyte solutions. The goal of this study is to define the parameters relevant for this force field, and their respective influence on the accuracy of the simulation. Simulations have been performed for extended ranges of these parameters and the results are compared to theoretical models. Finally, the trade-offs between optimal algorithmic efficiency and accuracy are analyzed.

Original language	English (US)
Pages (from-to)	179-183
Number of pages	5
Journal	Journal of Computational Electronics
Volume	4
Issue number	1-2
DOIs	https://doi.org/10.1007/s10825-005-7134-5
State	Published - Apr 2005
Externally published	Yes

Keywords

Brownian dynamics
Force field scheme
Simulation of biological systems

ASJC Scopus subject areas

Electronic, Optical and Magnetic Materials
Atomic and Molecular Physics, and Optics
Modeling and Simulation
Electrical and Electronic Engineering

Access to Document

10.1007/s10825-005-7134-5

Cite this

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abstract = "The ability to accurately simulate electrolyte solutions is a strong requirement for the modeling of charge transport in ion channels. In this work, a Particle-Particle-Particle-Mesh (P3M) algorithm is used to model the electrostatic interactions governing the physics of electrolyte solutions. The goal of this study is to define the parameters relevant for this force field, and their respective influence on the accuracy of the simulation. Simulations have been performed for extended ranges of these parameters and the results are compared to theoretical models. Finally, the trade-offs between optimal algorithmic efficiency and accuracy are analyzed.",

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AU - Marreiro, David

AU - Aboud, Shela

AU - Saraniti, Marco

AU - Eisenberg, Robert

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N2 - The ability to accurately simulate electrolyte solutions is a strong requirement for the modeling of charge transport in ion channels. In this work, a Particle-Particle-Particle-Mesh (P3M) algorithm is used to model the electrostatic interactions governing the physics of electrolyte solutions. The goal of this study is to define the parameters relevant for this force field, and their respective influence on the accuracy of the simulation. Simulations have been performed for extended ranges of these parameters and the results are compared to theoretical models. Finally, the trade-offs between optimal algorithmic efficiency and accuracy are analyzed.

AB - The ability to accurately simulate electrolyte solutions is a strong requirement for the modeling of charge transport in ion channels. In this work, a Particle-Particle-Particle-Mesh (P3M) algorithm is used to model the electrostatic interactions governing the physics of electrolyte solutions. The goal of this study is to define the parameters relevant for this force field, and their respective influence on the accuracy of the simulation. Simulations have been performed for extended ranges of these parameters and the results are compared to theoretical models. Finally, the trade-offs between optimal algorithmic efficiency and accuracy are analyzed.

KW - Brownian dynamics

KW - Force field scheme

KW - Simulation of biological systems

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